.TH g_densmap 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_densmap - calculates 2D planar or axial-radial density maps

.B VERSION 4.5
.SH SYNOPSIS
\f3g_densmap\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-od" " densmap.dat "
.BI "\-o" " densmap.xpm "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-bin" " real "
.BI "\-aver" " enum "
.BI "\-xmin" " real "
.BI "\-xmax" " real "
.BI "\-n1" " int "
.BI "\-n2" " int "
.BI "\-amax" " real "
.BI "\-rmax" " real "
.BI "\-[no]mirror" ""
.BI "\-[no]sums" ""
.BI "\-unit" " enum "
.BI "\-dmin" " real "
.BI "\-dmax" " real "
.SH DESCRIPTION
\&g_densmap computes 2D number\-density maps.
\&It can make planar and axial\-radial density maps.
\&The output \fB .xpm\fR file can be visualized with for instance xv
\&and can be converted to postscript with xpm2ps.
\&Optionally, output can be in text form to a .dat file.
\&


\&The default analysis is a 2\-D number\-density map for a selected
\&group of atoms in the x\-y plane.
\&The averaging direction can be changed with the option \fB \-aver\fR.
\&When \fB \-xmin\fR and/or \fB \-xmax\fR are set only atoms that are
\&within the limit(s) in the averaging direction are taken into account.
\&The grid spacing is set with the option \fB \-bin\fR.
\&When \fB \-n1\fR or \fB \-n2\fR is non\-zero, the grid
\&size is set by this option.
\&Box size fluctuations are properly taken into account.
\&


\&When options \fB \-amax\fR and \fB \-rmax\fR are set, an axial\-radial
\&number\-density map is made. Three groups should be supplied, the centers
\&of mass of the first two groups define the axis, the third defines the
\&analysis group. The axial direction goes from \-amax to +amax, where
\&the center is defined as the midpoint between the centers of mass and
\&the positive direction goes from the first to the second center of mass.
\&The radial direction goes from 0 to rmax or from \-rmax to +rmax
\&when the \fB \-mirror\fR option has been set.
\&


\&The normalization of the output is set with the \fB \-unit\fR option.
\&The default produces a true number density. Unit \fB nm\-2\fR leaves out
\&the normalization for the averaging or the angular direction.
\&Option \fB count\fR produces the count for each grid cell.
\&When you do not want the scale in the output to go
\&from zero to the maximum density, you can set the maximum
\&with the option \fB \-dmax\fR.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-od" " densmap.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-o" " densmap.xpm" 
.B Output
 X PixMap compatible matrix file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-bin"  " real" " 0.02  " 
 Grid size (nm)

.BI "\-aver"  " enum" " z" 
 The direction to average over: \fB z\fR, \fB y\fR or \fB x\fR

.BI "\-xmin"  " real" " \-1    " 
 Minimum coordinate for averaging

.BI "\-xmax"  " real" " \-1    " 
 Maximum coordinate for averaging

.BI "\-n1"  " int" " 0" 
 Number of grid cells in the first direction

.BI "\-n2"  " int" " 0" 
 Number of grid cells in the second direction

.BI "\-amax"  " real" " 0     " 
 Maximum axial distance from the center

.BI "\-rmax"  " real" " 0     " 
 Maximum radial distance

.BI "\-[no]mirror"  "no    "
 Add the mirror image below the axial axis

.BI "\-[no]sums"  "no    "
 Print density sums (1D map) to stdout

.BI "\-unit"  " enum" " nm\-3" 
 Unit for the output: \fB nm\-3\fR, \fB nm\-2\fR or \fB count\fR

.BI "\-dmin"  " real" " 0     " 
 Minimum density in output

.BI "\-dmax"  " real" " 0     " 
 Maximum density in output (0 means calculate it)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
